Influenza A viruses (IAV) are significant human pathogens causing yearly epidemics and occasional pandemics. Past pandemics have resulted in significant morbidity and mortality. The 1918 influenza pandemic was thought to have resulted in the death of at least 675,000 people in the U.S., and 40 million people worldwide. Annual influenza A virus epidemics are also very significant, resulting in approximately 30,000 deaths in the U.S. per year. Pandemic strains of influenza emerge periodically and are thought to be derived ultimately from avian influenza A viruses. The current 2009 pandemic influenza virus emerged by reassortment of two pre-existing swine influenza virus lineages. The first lineage is the European avian-like swine lineage which emerged from an avian influenza virus in toto. The second lineage is the triple-reassortant H1N2 swine influenza virus containing gene segments derived from avian, human, and classical swine influenza viruses. The natural reservoir of influenza A viruses is thought to be wild waterfowl. Genetically and antigenically diverse influenza A viruses circulate in wild birds and viral strains from this pool can adapt to new hosts, including humans and domestic animals. Influenza A viruses are also significant pathogens for agriculturally important animals like poultry, swine, and horses. Understanding the mechanisms of host switching are very important for surveillance and pandemic preparedness. Understanding the molecular basis underlying the annual evolution of human influenza will aid in vaccine strain selection. Avian influenza A virus evolutionary biology: We are currently evaluating the molecular epidemiology of approximately 50 avian influenza viruses isolated from the same population of birds over a several month period in 2006. Low pathogenicity avian influenza viruses of both H5N1 and H7N3 subtypes were isolated. These subtypes have been associated with highly pathogenic avian influenza virus outbreaks. We have generated complete genomic sequences from these isolates and are examining their phylogenetic relationships in comparison to approximately 500 other complete avian influenza virus genomes to examine questions of reassortment and gene flow in wild bird influenza viruses. Work performed previously in this project demonstrated that avian influenza A viruses in wild birds form transient genome constellations, continually reshuffled by reassortment, in contrast to the spread of a limited number of stable genome constellations that characterizes the evolution of mammalian-adapted IAV. The current analysis adds further support to this hypothesis. Thus it is likely that avian IAV in wild birds exists as a large pool of functionally equivalent, and often inter-changeable, gene segments that form transient genome constellations, without the strong selective pressure to be maintained as linked genomes. Swine influenza A virus evolutionary biology: In 1979, a lineage of avian-like H1N1 influenza A viruses emerged in European swine populations independently from the classical swine H1N1 virus lineage that had circulated in pigs since the Spanish influenza pandemic of 1918. To determine whether these two distinct lineages of swine-adapted A/H1N1 viruses evolved from avian-like A/H1N1 ancestors in similar ways, as might be expected given their common host species and origin, we compared patterns of nucleotide and amino acid change in whole genome sequences of both groups. An analysis of nucleotide compositional bias across all eight genomic segments for the two swine lineages showed a clear lineage-specific bias, although a segment-specific effect was also apparent. As such, there appears to be only a relatively weak host-specific selection pressure. Strikingly, despite each lineage evolving in the same species of host for decades, amino acid analysis revealed little evidence of either parallel or convergent changes. These findings suggest that although adaptation due to evolutionary lineages can be distinguished, there are functional and structural constraints on all gene segments and that the evolutionary trajectory of each lineage of swine A/H1N1 virus has a strong historical contingency. Thus, in the context of emergence of an influenza A virus strain via a host switch event, it is difficult to predict what specific polygenic changes are needed for mammalian adaptation. Examination of the evolutionary dynamics of swine influenza is crucial to understanding the emergence of the 2009 pandemic influenza virus which was the result of a reasortment event between the above studied European influenza viral lineage and an independent, triple-reassortant swine influenza viral lineage circulating in North America.